chr1-74764007-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_138467.3(TYW3):c.674A>G(p.Glu225Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000261 in 1,611,612 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_138467.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TYW3 | NM_138467.3 | c.674A>G | p.Glu225Gly | missense_variant | 6/6 | ENST00000370867.8 | |
TYW3 | NM_001162916.2 | c.575A>G | p.Glu192Gly | missense_variant | 5/5 | ||
TYW3 | XM_006710347.3 | c.674A>G | p.Glu225Gly | missense_variant | 6/7 | ||
TYW3 | NR_027962.2 | n.880A>G | non_coding_transcript_exon_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TYW3 | ENST00000370867.8 | c.674A>G | p.Glu225Gly | missense_variant | 6/6 | 1 | NM_138467.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000145 AC: 22AN: 152126Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00000804 AC: 2AN: 248754Hom.: 0 AF XY: 0.00000744 AC XY: 1AN XY: 134344
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1459486Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 725912
GnomAD4 genome ? AF: 0.000145 AC: 22AN: 152126Hom.: 1 Cov.: 32 AF XY: 0.000215 AC XY: 16AN XY: 74304
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 28, 2023 | The c.674A>G (p.E225G) alteration is located in exon 6 (coding exon 6) of the TYW3 gene. This alteration results from a A to G substitution at nucleotide position 674, causing the glutamic acid (E) at amino acid position 225 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at